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Author Topic:   How to make a ribozyme (using abiotic starting compounds)
Rob 
Suspended Member (Idle past 5849 days)
Posts: 2297
Joined: 06-01-2006


Message 16 of 55 (410741)
07-17-2007 2:51 AM
Reply to: Message 15 by Doddy
07-16-2007 5:33 AM


Re: Synthesis of Nucleosides
Doddy
I don't care how smart you think humans are, or how dumb you think chemical reactions are - I have no problem believing that this would have happened.
Thanks Doddy... I appriciate the fact that you at least have the intellectual honesty to admit that it is a 'belief', and not dogmatically state it as fact. There is nothing wrong with belief. But calling belief fact is another matter.
And there are several ways to test belief that when incorportated into a whole test, are quite powerful; Emperical adequacy, Logical coherence, and experiential relevance.
Personally, I have a big problem believing it could happen without intelligent guidance, because it is 'counter emperical' to believe that nature organizes anything. Nature tears down. The fact that organisms exist does not 'prove' that nature did it. Life is itself, a big '?'.
And these organisms are the most highly organized systems that we know of (And I just mean the single celled ones, at the genetic level). But, we are talking once again about my 'belief'.
There may be information out there that would change the playing field, but we don't have it. The information that we do have (ie emperical) says no. In particular the 2nd Law of Thermodnamics.
To presuppose (unscientifically but rather philosophically) that everything is material in origin is also falacious. To exclude philosophical coherence as a valid test, purely on philosophical grounds does not follow. It is utterly illogical.
What troubles me, is that too many have moved past the problem (a very big problem I might add) with full conviction that it will be solved.
We don't move to B until you have A. If we do, it is nothing but theatre.
Doddy
However, it isn't especially likely that life originated in this manner. Not only are these steps quite probably not the ones that occurred, but a ribozyme might not even be the first sort of life (if the RNA world isn't true).
Especially since every component in the cell, is produced by the code in the DNA in conjunction with the other macinery in the cell. Even RNA is transcribed from the DNA, no? So what good is RNA on it's own.
The smallest self replicating system that is emperical already exists. What are the implications if no other form exists (a negative affirmation that cannot be proven)? But for arguments sake... what are the implications?
I ask, because the same unproveable argument is made 'by some', that since there is no emperical evidence for God (nevermind our infinite universe) the we must assume he does not exist.
Why can't we assume that no other self replicating cycle exists, because we have no evidence of one?
You end up needing a whole bunch of different but coincidentally compatible RNAs (in some form) that converge in the same time and space. I know your familliar with all of this... I just confess complete incredulity.
Even Molbiogirl's reference in the other thread admitted, in the details, that we needed this, and then that etc... There's just no such thing as self-organizing. And to me it is just as unlikely as a perpetual motion machine, that not only perpetuates, but also grows. It's a bad analogy... but it makes the point.
I don't want to deride anyone for the effort being expended to do research, but I do have one question that I would appriciate an answer to.
All of this aside, let's assume that you (or anyone else) were able to solve this problem. I can't help but wonder... why do you want to solve it?

This message is a reply to:
 Message 15 by Doddy, posted 07-16-2007 5:33 AM Doddy has replied

Replies to this message:
 Message 17 by DrJones*, posted 07-17-2007 3:42 AM Rob has replied
 Message 19 by Doddy, posted 07-17-2007 5:28 AM Rob has replied

  
DrJones*
Member
Posts: 2284
From: Edmonton, Alberta, Canada
Joined: 08-19-2004
Member Rating: 6.8


Message 17 of 55 (410749)
07-17-2007 3:42 AM
Reply to: Message 16 by Rob
07-17-2007 2:51 AM


Re: Synthesis of Nucleosides
In particular the 2nd Law of Thermodnamics
Come on Rob, you've been here long enough to know that this is bullshit. The 2nd law of thermo applies to closed systems, the Earth is not a closed system.

Just a monkey in a long line of kings.
If "elitist" just means "not the dumbest motherfucker in the room", I'll be an elitist!
*not an actual doctor

This message is a reply to:
 Message 16 by Rob, posted 07-17-2007 2:51 AM Rob has replied

Replies to this message:
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 Message 20 by Rob, posted 07-18-2007 1:18 AM DrJones* has replied

  
anglagard
Member (Idle past 836 days)
Posts: 2339
From: Socorro, New Mexico USA
Joined: 03-18-2006


Message 18 of 55 (410751)
07-17-2007 4:00 AM
Reply to: Message 17 by DrJones*
07-17-2007 3:42 AM


Re: Synthesis of Nucleosides
Dr Jones writes:
Come on Rob, you've been here long enough to know that this is bullshit. The 2nd law of thermo applies to closed systems, the Earth is not a closed system.
“If you tell a lie big enough and keep repeating it, people will eventually come to believe it. The lie can be maintained only for such time as the State can shield the people from the political, economic and/or military consequences of the lie. It thus becomes vitally important for the State to use all of its powers to repress dissent, for the truth is the mortal enemy of the lie, and thus by extension, the truth is the greatest enemy of the State.”
Joseph Goebbels.
“A lie told often enough becomes truth”
Vladimir Lenin.
Strange bedfellows, but then again strange interpretations concerning "bearing false witness."

This message is a reply to:
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Doddy
Member (Idle past 5909 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 19 of 55 (410756)
07-17-2007 5:28 AM
Reply to: Message 16 by Rob
07-17-2007 2:51 AM


Re: Synthesis of Nucleosides
Rob writes:
it is 'counter emperical' to believe that nature organizes anything. Nature tears down.
The very definition of life, as proposed by Schrdinger, is something that organised itself - negative entropy. However, negative entropy is not restricted to life. Snowflakes are an example, but I think a better one is galaxies - the force of gravity caused them to organise, forming a lower entropy state. It isn't to hard to imagine, at least for myself, that such a low entropy state would happen upon a formation that could indeed become reproducible (in that life must grow).
Rob writes:
The information that we do have (ie emperical) says no. In particular the 2nd Law of Thermodnamics.
As Dr Jones* tried to point out, albeit slight erroneously, life itself isn't prohibited by the second law. DrJones* was right in that the particular interpretation of the second law stating "everything tends to a higher entropy state" only applies to closed systems, although the law has no problem dealing with open systems - you just need to factor in the enthalpy change too.
Rob writes:
To presuppose (unscientifically but rather philosophically) that everything is material in origin is also falacious. To exclude philosophical coherence as a valid test, purely on philosophical grounds does not follow. It is utterly illogical.
To discuss this in depth would drag the thread off topic, but suffice it to say that supernatural things are not only beyond the scope of science, but indeed one must presuppose their non-existence if one intends to investigate the natural world. Else, one can never be sure if one is observing the natural or the supernatural world, thus making all experiments meaningless.
Rob writes:
Especially since every component in the cell, is produced by the code in the DNA in conjunction with the other macinery in the cell. Even RNA is transcribed from the DNA, no? So what good is RNA on it's own.
The fact that certain conformations of RNA are able to reproduce others is precisely what drives the RNA world hypothesis. That is why I asked to make a ribozyme, as it is an RNA molecule that can make another RNA molecule. It is DNA that is dependant on RNA, not the other way around, as a strand of DNA cannot, IIRC, be created by itself, but must extend from an RNA molecule (which is then degraded to be replaced with DNA).
Rob writes:
What are the implications if no other form exists (a negative affirmation that cannot be proven)? But for arguments sake... what are the implications?
It is unlikely that current life-forms are the simplest form of replication that can exist. Just as I would say that current media players (eg an iPod) are unlikely to be the simplest that exist (a record player? a phonograph?). It is only those lifeforms that are complicated enough to survive for billions of years that will be seen today, not the simplest ones.
Rob writes:
Why can't we assume that no other self replicating cycle exists, because we have no evidence of one?
But we do have evidence for one - we see a self-replicating cycle, and it is only extrapolation backwards that leads to the assumption of one existing. It's an entirely different thing with supernatural beings, but I fear dragging this thread off the rails if I elaborate.
Rob writes:
You end up needing a whole bunch of different but coincidentally compatible RNAs (in some form) that converge in the same time and space. I know your familliar with all of this... I just confess complete incredulity.
Oh yeah, that is the case. It's not extremely unlikely, but I wouldn't have money on it, personally. After all, the areas where one RNA molecule would exist are likely to be friendly to others. It is also likely that this didn't occur in a vast ocean, but a small pond or something. But yeah, it's not likely, but it's possible.
Rob writes:
There's just no such thing as self-organizing.
Bold words coming from a self-organizing system such as yourself!
Rob writes:
And to me it is just as unlikely as a perpetual motion machine, that not only perpetuates, but also grows. It's a bad analogy... but it makes the point.
As I said above, a self-perpetuating low entropy anomaly violates no known law of physics, whereas a perpetual motion machine does.
Rob writes:
All of this aside, let's assume that you (or anyone else) were able to solve this problem. I can't help but wonder... why do you want to solve it?[
Why not? Knowledge is good.

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This message is a reply to:
 Message 16 by Rob, posted 07-17-2007 2:51 AM Rob has replied

Replies to this message:
 Message 21 by Rob, posted 07-18-2007 1:27 AM Doddy has replied
 Message 26 by Rob, posted 07-22-2007 1:24 AM Doddy has replied

  
Rob 
Suspended Member (Idle past 5849 days)
Posts: 2297
Joined: 06-01-2006


Message 20 of 55 (410929)
07-18-2007 1:18 AM
Reply to: Message 17 by DrJones*
07-17-2007 3:42 AM


Re: Synthesis of Nucleosides
DJ
The 2nd law of thermo applies to closed systems, the Earth is not a closed system.
Seems to me you've dramaitcally oversimplified the issue in the same manner that those who hypothesize the synthesis of nucleosides do...
The first Law of Thermodynamics clearly states that energy can neither be created nor destroyed. Therefore, within a purely naturalistic framework, the universe as a whole is a closed system.
Therefore the second law means the clock is ticking...
And the earth resides within the universe the last time I checked. I don't think we're exempt from the law.
The only thing keeping entropy at bay on earth is intelligence. And not our intelligence btw, but whoever or whatever programmed life (in particular, giving plants the ability to harness the energy in light).
Life is the only thing... fighting against that which is trying to kill it; organizing and reorganizing that which nature (governed by the 2nd law) is in the process of breaking down. And break down it will.
I just don't understand where your coming from...
Is this the appropriate thread in which to discuss this since it relates to the topic, or is it too much a tangent?
What you are suggesting is not emperical but theoretical. What is emperical, is that intelligence and highly organized systems can resist entropy, but not defeat it. We're slowly losing...
Show me where we're slowly winning?
Am I missing something?

This message is a reply to:
 Message 17 by DrJones*, posted 07-17-2007 3:42 AM DrJones* has replied

Replies to this message:
 Message 22 by DrJones*, posted 07-18-2007 1:43 AM Rob has not replied
 Message 23 by iceage, posted 07-18-2007 1:44 AM Rob has not replied
 Message 24 by NosyNed, posted 07-18-2007 1:48 AM Rob has not replied

  
Rob 
Suspended Member (Idle past 5849 days)
Posts: 2297
Joined: 06-01-2006


Message 21 of 55 (410930)
07-18-2007 1:27 AM
Reply to: Message 19 by Doddy
07-17-2007 5:28 AM


Re: Synthesis of Nucleosides
Doddy, I am going to work on some of your comments at a later date. i don't have the energy to unwind them at the moment. And something tells me that my last response to DJ is going to cause me some research beofre this is over...
For now, I did have to respond to one of your comments....
Rob writes:
All of this aside, let's assume that you (or anyone else) were able to solve this problem. I can't help but wonder... why do you want to solve it?
Doddy Why not? Knowledge is good.
I must say Doddy... I would have expected such anti-depth from the script of a low budget flick... but not from you.
I didn't ask that question for my benefit... but your own.

This message is a reply to:
 Message 19 by Doddy, posted 07-17-2007 5:28 AM Doddy has replied

Replies to this message:
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DrJones*
Member
Posts: 2284
From: Edmonton, Alberta, Canada
Joined: 08-19-2004
Member Rating: 6.8


Message 22 of 55 (410931)
07-18-2007 1:43 AM
Reply to: Message 20 by Rob
07-18-2007 1:18 AM


Re: Synthesis of Nucleosides
Is this the appropriate thread in which to discuss this since it relates to the topic, or is it too much a tangent?
There are several other threads that cover why the 2nd law of thermo arguement as put forth by ID/creation-ists is bullshit, its not really on topic here.
Edited by DrJones*, : No reason given.

Just a monkey in a long line of kings.
If "elitist" just means "not the dumbest motherfucker in the room", I'll be an elitist!
*not an actual doctor

This message is a reply to:
 Message 20 by Rob, posted 07-18-2007 1:18 AM Rob has not replied

  
iceage 
Suspended Member (Idle past 5915 days)
Posts: 1024
From: Pacific Northwest
Joined: 09-08-2003


Message 23 of 55 (410932)
07-18-2007 1:44 AM
Reply to: Message 20 by Rob
07-18-2007 1:18 AM


Re: Synthesis of Nucleosides
Rob writes:
The only thing keeping entropy at bay on earth is intelligence.
Life is a net entropy producer. Life just positions itself between the flow of energy from a high quality to a low quality and makes something ordered and useful in between.
Consider the grading of beach sand. Wave action will sort out the different size grains - which is an increase of order or decrease in entropy. This grading is not a violation of the 2nd law, nor is it "keeping entropy at bay", but just an intermediate result of energy dissipation.

This message is a reply to:
 Message 20 by Rob, posted 07-18-2007 1:18 AM Rob has not replied

  
NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 24 of 55 (410933)
07-18-2007 1:48 AM
Reply to: Message 20 by Rob
07-18-2007 1:18 AM


pontificating inappropriately
Rob, it might be an idea if you stopped going on about topics which you clearly haven't got a very solid grasp of. Clearly thermodynamics is one of those.
Intelligence is not what is "keeping entropy at bay". The available energy of the sun is what is doing it.
We are, of course, slowly losing if you take a very big view.
As for why we want to learn anything: It is just as Doddy said "knowledge is good". I find it just feels good to learn things. It's better than a cold beer.

This message is a reply to:
 Message 20 by Rob, posted 07-18-2007 1:18 AM Rob has not replied

  
Doddy
Member (Idle past 5909 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 25 of 55 (410943)
07-18-2007 3:42 AM
Reply to: Message 21 by Rob
07-18-2007 1:27 AM


Re: Synthesis of Nucleosides
Rob writes:
I must say Doddy... I would have expected such anti-depth from the script of a low budget flick... but not from you.
I didn't ask that question for my benefit... but your own.
I'm sorry, but that is the entirety of it. Speaking for myself, however. I'm just curious about this stuff. I'm sure much the same reason applies to other scientists. Plus, it helps me learn about organic chemistry.
What answer did you expect? "We want to learn about this so that we can better support our materialistic worldview by explaining how life doesn't need a creator."

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Rob 
Suspended Member (Idle past 5849 days)
Posts: 2297
Joined: 06-01-2006


Message 26 of 55 (411714)
07-22-2007 1:24 AM
Reply to: Message 19 by Doddy
07-17-2007 5:28 AM


Re: Synthesis of Nucleosides
Rob writes:
Why can't we assume that no other self replicating cycle exists, because we have no evidence of one?
But we do have evidence for one - we see a self-replicating cycle, and it is only extrapolation backwards that leads to the assumption of one existing. It's an entirely different thing with supernatural beings, but I fear dragging this thread off the rails if I elaborate.
I can understand that... it is reasonable.
But it is exactly this 'extrapolation' that is purely 'theo' and is not science (even in terms of the current convention of methodological naturalism). As you said before, it is a belief. It is the same theological foundation that the apostle Paul used in romans chapter 1. I'll spare you the details since I have Romans chapter 1 at least 6 times in the recent past.
Even so, I think I found the difference, and it relates to the 2nd law of thermodynamics as well (which I will have to address at another time and in another thread). Your talking about a self replicating cycle (and so was I)... I think we must distinguish between a self replicating cycle, and a self organizing cycle.
A self replicating cycle is easy really, but it comes after the organization of the system. What do you think?
Rob writes:
There's just no such thing as self-organizing.
Bold words coming from a self-organizing system such as yourself!
That's what I mean right there... I am not self organizing. I am self replicating...

This message is a reply to:
 Message 19 by Doddy, posted 07-17-2007 5:28 AM Doddy has replied

Replies to this message:
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 Message 28 by Doddy, posted 07-22-2007 3:14 AM Rob has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 27 of 55 (411720)
07-22-2007 1:54 AM
Reply to: Message 26 by Rob
07-22-2007 1:24 AM


Re: Synthesis of Nucleosides
That's what I mean right there... I am not self organizing.
Who organized you, then?

This message is a reply to:
 Message 26 by Rob, posted 07-22-2007 1:24 AM Rob has not replied

  
Doddy
Member (Idle past 5909 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 28 of 55 (411723)
07-22-2007 3:14 AM
Reply to: Message 26 by Rob
07-22-2007 1:24 AM


Re: Synthesis of Nucleosides
Rob writes:
But it is exactly this 'extrapolation' that is purely 'theo' and is not science (even in terms of the current convention of methodological naturalism).
Extrapolation is scientific. It is assuming something without any evidence from which to extrapolate or interpolate that isn't.
Rob writes:
I think we must distinguish between a self replicating cycle, and a self organizing cycle.
A self replicating cycle is easy really, but it comes after the organization of the system. What do you think?
What is the difference? In order for something to replicate, it must go from one organised entity to two organised entities. Thus, it must have a mechanism of organisation - anabolism ('organising' reactions). Replication is just one major form of this type of metabolism. So replication is self-organization.
It is possible that anabolism precedes replication, but this thread shall assume otherwise for the reason that most research has been done on the replicator-first hypothesis.

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This message is a reply to:
 Message 26 by Rob, posted 07-22-2007 1:24 AM Rob has replied

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Rob 
Suspended Member (Idle past 5849 days)
Posts: 2297
Joined: 06-01-2006


Message 29 of 55 (411745)
07-22-2007 9:21 AM
Reply to: Message 28 by Doddy
07-22-2007 3:14 AM


Re: Synthesis of Nucleosides
[qs]
Rob writes
But it is exactly this 'extrapolation' that is purely 'theo' and is not science (even in terms of the current convention of methodological naturalism).
Doddy: Extrapolation is scientific. It is assuming something without any evidence from which to extrapolate or interpolate that isn't.
Not really... extrapolation is 'theo' (or 'theo'ry if you prefer). It is an 'inference to the best explanation'.
Now please listen carefully for a moment because I do not want to be misunderstood.... Extrapolation based upon fact may be reasonable and logical, but that is only if we assume philosophical coherence and logic to be a valid 'scientific proof' of an ideas worth.
Personally, I do believe so. So if science is determined to be logical, I am with you.
Furthermore, since the only time we see language and code being 'written', is in the presence of intelligence, we can extrapolate from what we do know that the origin of biological structures such as DNA (a quaternary code / language) arose from intelligence.
So I agree with your coherent and valid philosophical basis for your argument Doddy. But why can't those in ID, use the same argument as a 'scientifically valid inference' for design?
This argument is well presented here for those interested: Abiogenesis Just scroll down to the man writing on the chaulkboard (which is part 5 of 7), then click the play button in the middle of the YouTube player. After it begins to play, click the menu button in the lower right corner and click on part 7 of 7. The argument is given about 2 minutes into the clip though it is helpful to see clip 6 and 7 respectively to grasp the entire context.
So both intelligent design 'theory', as well as 'evolutionary theory', are an extrapolation from the facts. They are inferences based upon what is known, so as to see what is not known.
The only difference between them, is that ID is ultimately more coherent logically, in spite of any presuppositions or 'wishes' of the observers.
Methodological naturalism is ultimately forced to assume (without explanation) that the material universe (simply because of it's eternal nature) was bound or predetermined to self organize at some point.
And that is interesting because a Christian such as myself would say (also without much explantion) that it is simply God's eternal nature to have self existed eternally, and to create in an organized and intelligeble manner.
No difference in terms of faith, ultimately...
The only real difference, is in the questions of 'meaning'. And though science acts as though meaning is irrelevant to science, I cannot help but wonder what they mean by that...
The implications of we being the ultimate intelligence or not, are quite staggering. The implications are very distinct between the two worldviews.
Rob writes: I think we must distinguish between a self replicating cycle, and a self organizing cycle.
A self replicating cycle is easy really, but it comes after the organization of the system. What do you think?
Doddy: What is the difference? In order for something to replicate, it must go from one organised entity to two organised entities. Thus, it must have a mechanism of organisation - anabolism ('organising' reactions). Replication is just one major form of this type of metabolism. So replication is self-organization.
Come now, what happened to logical extrapolation already?
Replication is simply copying what already exists. The 'mechanisms' and preplication is regulated by a preexisting code and organization. What is the origin of the order which dictates the replication?
What we can know for sure (logically) is that replication is not the source of the order, for there would be nothing to replicate. Replication is not creation. Before something can be replicated... it must exist.
If you want to assume the existence of order and intelligence as the source of the first cause, then you must look to the only place that has offered a coherent explanation, and that is the doctrine of the Trinitarian God. And His is a strange and alien metabolism indeed. A consuming fire is how some were inspired to describe Him.
Not an indifferent and mindless material reality, but a living mind that sees and knows all. Logic Himself is alive and stalking you and I to test our deep and hidden motives.
But that is only valid if philosophical coherence is king, and the facts being necessarily bound to fit inside of the logical box.
If we want to force open that box, and be free in an unlimited way, we will bear the fruit of the disorder and illogic that follows.
Eat anything in the garden... just leave that one fruit (questioning the validity of logic) alone. If we question philosphical coherence, what then can be true? Our own bias based upon personal and selfish motives?
Order and logic is not a prison. Disorder on the other hand, is to ultimately not think, or be, at all.
Here's the point Doddy... And it follows from top to bottom. In this case it is nucleotide synthesis but it is logic we must look to for guidance. I see a lot of deconstruction going on here at EVC. But to deconstruct, we must first, start with a 'construct'.
It takes intelligence to start putting the pieces together. Don't just look at the pieces, look at the big picture regardless of what Nosy thinks.

This message is a reply to:
 Message 28 by Doddy, posted 07-22-2007 3:14 AM Doddy has replied

Replies to this message:
 Message 30 by Percy, posted 07-22-2007 10:02 AM Rob has replied
 Message 41 by Doddy, posted 07-23-2007 1:33 AM Rob has replied

  
Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 30 of 55 (411746)
07-22-2007 10:02 AM
Reply to: Message 29 by Rob
07-22-2007 9:21 AM


Re: Synthesis of Nucleotides
Rob writes:
Furthermore, since the only time we see language and code being 'written', is in the presence of intelligence, we can extrapolate from what we do know that the origin of biological structures such as DNA (a quaternary code / language) arose from intelligence.
Mutations, and there are a many different kinds of mutation from single nucleotide replacement to entire chromosome duplication, modify the genetic code. Almost every reproductive event introduces mutations without any intelligent participation. Extrapolation of the processes of mutation and selection backward in time is used as a framework in which to interpret life's change and diversity, including the origin of life itself.
Mutation is a predominantly random process we've actually confirmed observationally, and it relies only upon matter and energy following known physical laws, so scientific theories of life's origins are strongly based upon real-world evidence, though they remain extremely tentative at this point.
Intelligent design and intervention in the reproductive process in order to cause mutations has never been observed, and so theories that assume this happens are not based upon real-world evidence. Such theories require entities and processes to exist for which we have no evidence, neither direct nor indirect.
So I agree with your coherent and valid philosophical basis for your argument Doddy. But why can't those in ID, use the same argument as a 'scientifically valid inference' for design?
Because it assumes an intelligent agent without necessity. The genetic structures cited as evidence for ID form naturally. There is no necessity for arguing that objects fall because of intervention by intelligent agents, because we know about gravity. And there is no necessity for arguing that sequences of mutations happen because of intelligent intervention, because we know that mutations followed by selection happen naturally with no intervention whatsoever in generation after generation.
So both intelligent design 'theory', as well as 'evolutionary theory', are an extrapolation from the facts. They are inferences based upon what is known, so as to see what is not known.
What fact or facts or implication of facts is the introduction of an intelligent agent based upon?
--Percy

This message is a reply to:
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